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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ), 'gf_id' => 'HOM05D001473', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001473' ), 'data_identifier' => 'HOM05D001473', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001473', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '430', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A05p42950' => 'bna', 'A06p05590' => 'bna', 'A06p06440' => 'bna', 'A08p34350' => 'bna', 'A08p35050' => 'bna', 'A09p17580' => 'bna', 'A09p65810' => 'bna', 'Aa31LG1G5220' => 'aar', 'Aa31LG5G14960' => 'aar', 'Aa31sc889G10' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5606' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2394' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2481' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.307' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3249' => 'aag', 'Actinidia34748' => 'ach', 'Actinidia40002' => 'ach', 'Ah.04g163240' => 'amhyb', 'Ah.06g191880' => 'amhyb', 'AL1G19060' => 'aly', 'AL1G20320' => 'aly', 'AL3G14530' => 'aly', 'Aqoxy2G03659' => 'aox', 'Aqoxy5G00219' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0270XD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0LZD0Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.33TMW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8J7T4H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8L6PVU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9D2XZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E23V63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HJHY8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L81BKS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6YD0H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TZL30T' => 'arhy', 'AT1G08630' => 'ath', 'AT1G09770' => 'ath', 'AT3G04520' => 'ath', 'ATR0681G127' => 'atr', 'ATR0693G448' => 'atr', 'ATR0736G172' => 'atr', 'ATR0736G183' => 'atr', 'ATR0739G164' => 'atr', 'ATR0772G047' => 'atr', 'Atru.chr2.968' => 'acertr', 'Atru.chr2.969' => 'acertr', 'AUR62000484' => 'cqu', 'AUR62004850' => 'cqu', 'AUR62006826' => 'cqu', 'AUR62023607' => 'cqu', 'AUR62040934' => 'cqu', 'BcaB03g13321' => 'bca', 'BcaB03g13322' => 'bca', 'BcaB06g27306' => 'bca', 'BcaB07g31211' => 'bca', 'BcaB07g34104' => 'bca', 'BcaB08g37388' => 'bca', 'BcaB08g37389' => 'bca', 'BcaB08g37390' => 'bca', 'BcaC04g22223' => 'bca', 'BcaC05g29935' => 'bca', 'BcaC05g30190' => 'bca', 'BcaC05g30191' => 'bca', 'BcaC07g38404' => 'bca', 'BcaC07g38406' => 'bca', 'BcaC07g38437' => 'bca', 'BcaC07g41932' => 'bca', 'BolC1t01331H' => 'bol', 'BolC5t29431H' => 'bol', 'BolC5t29535H' => 'bol', 'BolC5t34926H' => 'bol', 'BolC8t48839H' => 'bol', 'BolC8t48842H' => 'bol', 'BolC8t48947H' => 'bol', 'BolC8t52518H' => 'bol', 'BolC9t55093H' => 'bol', 'BraA05t23040Z' => 'bra', 'BraA06t23767Z' => 'bra', 'BraA06t23855Z' => 'bra', 'BraA08t35347Z' => 'bra', 'BraA08t35414Z' => 'bra', 'BraA09t37388Z' => 'bra', 'BraA09t41925Z' => 'bra', 'C05p06710' => 'bna', 'C05p07840' => 'bna', 'C05p62730' => 'bna', 'C08p11600' => 'bna', 'C08p11640' => 'bna', 'C08p11680' => 'bna', 'C08p11970' => 'bna', 'C08p12030' => 'bna', 'C08p13180' => 'bna', 'C08p49900' => 'bna', 'C09p21880' => 'bna', 'CAN.G1363.10' => 'can', 'CAN.G1609.11' => 'can', 'CAN.G1609.5' => 'can', 'CAN.G1609.6' => 'can', 'CAN.G1609.7' => 'can', 'CAN.G1609.8' => 'can', 'CANSAT54G0715' => 'cansat', 'CANSAT54G1380' => 'cansat', 'CARHR008540' => 'chi', 'CARHR009740' => 'chi', 'CARHR078710' => 'chi', 'Carub.0001s0799' => 'cru', 'Carub.0001s0911' => 'cru', 'Carub.0003s0368' => 'cru', 'Ca_09455_v3' => 'car', 'Ca_09462_v3' => 'car', 'Ca_10017_v3' => 'car', 'Ca_29582_v3' => 'car', 'CBR_g39826' => 'cbr', 'Cc02_g08890' => 'ccan', 'Cc02_g08900' => 'ccan', 'CDE04G0210' => 'cde', 'CDE04G0538' => 'cde', 'CDE04G2649' => 'cde', 'CDE07G0773' => 'cde', 'Cfa002922' => 'cfa', 'Cfa006344' => 'cfa', 'Cfa024416' => 'cfa', 'Cfa025479' => 'cfa', 'Ciclev10018691m.g' => 'ccl', 'Ciclev10020798m.g' => 'ccl', 'CiPaw.04G081100' => 'cil', 'CiPaw.07G074300' => 'cil', 'ClCG02G017030' => 'cla', 'ClCG06G009580' => 'cla', 'ClCG06G009590' => 'cla', 'ClCG06G009620' => 'cla', 'COL.COLO4_15470' => 'col', 'COL.COLO4_15471' => 'col', 'COL.COLO4_24164' => 'col', 'Cpa.g.c29671.1' => 'cpa', 'Cpa.g.c29671.4' => 'cpa', 'Cpa.g.sc306.1' => 'cpa', 'Cpa.g.sc306.2' => 'cpa', 'Cpa.g.sc306.3' => 'cpa', 'Cre03.g197350' => 'cre', 'Cre10.g423550' => 'cre', 'CsaV3_1G045310' => 'csa', 'CsaV3_1G045320' => 'csa', 'CsaV3_1G045330' => 'csa', 'CsaV3_1G045340' => 'csa', 'CsaV3_1G045350' => 'csa', 'CsaV3_2G003740' => 'csa', 'CsaV3_UNG000020' => 'csa', 'CsaV3_UNG002020' => 'csa', 'CsaV3_UNG002030' => 'csa', 'CSS0002094' => 'camsi', 'CSS0002418' => 'camsi', 'CSS0012083' => 'camsi', 'CSS0020922' => 'camsi', 'CSS0022849' => 'camsi', 'CSS0023615' => 'camsi', 'CSS0024952' => 'camsi', 'CSS0026431' => 'camsi', 'CSS0031594' => 'camsi', 'CSS0041231' => 'camsi', 'CSS0044269' => 'camsi', 'CSS0044349' => 'camsi', 'CSS0046947' => 'camsi', 'DCAR_001202' => 'dca', 'DCAR_023095' => 'dca', 'DCAR_029377' => 'dca', 'Dinv05754' => 'din', 'Dinv18447' => 'din', 'Dinv18449' => 'din', 'Duzib106G0742' => 'dzi', 'Duzib106G1036' => 'dzi', 'Duzib128G0032' => 'dzi', 'Duzib177G0283' => 'dzi', 'Duzib177G0445' => 'dzi', 'ECA233G2045' => 'eca', 'ECA238G0750' => 'eca', 'EL10Ac4g09039' => 'bvu', 'EL10Ac4g09571' => 'bvu', 'Eucgr.B01570' => 'egr', 'Eucgr.H04236' => 'egr', 'FAN02G1215' => 'fan', 'FAN05G0714' => 'fan', 'FAN05G5604' => 'fan', 'FAN09G1753' => 'fan', 'FAN11G3850' => 'fan', 'FAN14G1026' => 'fan', 'FAN14G3813' => 'fan', 'FvH4_3g19200' => 'fve', 'FvH4_3g19210' => 'fve', 'FvH4_6g01941' => 'fve', 'FvH4_6g01950' => 'fve', 'Glyma.03G250800' => 'gma', 'Glyma.10G165900' => 'gma', 'Glyma.10G166000' => 'gma', 'Glyma.20G223200' => 'gma', 'Glyma.20G223300' => 'gma', 'Gohir.A11G247800' => 'ghi', 'Gohir.A11G247900' => 'ghi', 'Gohir.A11G247950' => 'ghi', 'Gohir.A11G299500' => 'ghi', 'Gohir.A13G167800' => 'ghi', 'Gohir.A13G167900' => 'ghi', 'Gohir.D11G258200' => 'ghi', 'Gohir.D11G258300' => 'ghi', 'Gohir.D11G314300' => 'ghi', 'Gohir.D13G173200' => 'ghi', 'Gohir.D13G173300' => 'ghi', 'Gorai.007G276400' => 'gra', 'Gorai.007G276500' => 'gra', 'Gorai.007G345500' => 'gra', 'Gorai.013G187200' => 'gra', 'Gorai.013G187300' => 'gra', 'GSVIVG01023525001' => 'vvi', 'GSVIVG01023526001' => 'vvi', 'GSVIVG01023527001' => 'vvi', 'HanXRQChr07g0194851' => 'han', 'HanXRQChr08g0225461' => 'han', 'HanXRQChr14g0455221' => 'han', 'Haze_04437' => 'cav', 'Haze_04445' => 'cav', 'Haze_04446' => 'cav', 'Haze_25281' => 'cav', 'Haze_25283' => 'cav', 'Haze_26225' => 'cav', 'Haze_27330' => 'cav', 'Haze_27403' => 'cav', 'Hma1.2p1_0075F.1_g039180' => 'hma', 'HPP92_012652' => 'vpl', 'HPP92_023254' => 'vpl', 'HPP92_023312' => 'vpl', 'HPP92_023313' => 'vpl', 'HPP92_023314' => 'vpl', 'Hund06911' => 'sun', 'Hund07267' => 'sun', 'Hund22157' => 'sun', 'Lalb_Chr02g0149081' => 'lal', 'Lalb_Chr06g0168271' => 'lal', 'Lalb_Chr15g0076051' => 'lal', 'Lalb_Chr18g0044021' => 'lal', 'Lalb_Chr21g0311171' => 'lal', 'Lj1g0008177' => 'lja', 'Lj1g0012496' => 'lja', 'Lj1g0014796' => 'lja', 'Lj5A229T66' => 'lonja', 'Lj5A229T67' => 'lonja', 'Lj5g0018401' => 'lja', 'Lj5g0024997' => 'lja', 'Lj8C196T8' => 'lonja', 'Lsat_1_v5_gn_1_80541' => 'lsa', 'Lsat_1_v5_gn_2_108040' => 'lsa', 'Lsat_1_v5_gn_4_66321' => 'lsa', 'Lsat_1_v5_gn_5_132420' => 'lsa', 'Lsat_1_v5_gn_5_135881' => 'lsa', 'Lsat_1_v5_gn_8_2880' => 'lsa', 'Lsat_1_v5_gn_8_72320' => 'lsa', 'Lsat_1_v5_gn_8_99221' => 'lsa', 'Manes.08G139000' => 'mes', 'Manes.08G139200' => 'mes', 'Manes.09G148300' => 'mes', 'Manes.09G148400' => 'mes', 'Mapoly0014s0195' => 'mpo', 'Mapoly0128s0013' => 'mpo', 'MBI07_g16923_MAGBIO' => 'mbi', 'MCO01G096' => 'mco', 'MCO01G097' => 'mco', 'MCO14G222' => 'mco', 'MD04G1229500' => 'mdo', 'MD12G1246400' => 'mdo', 'MD12G1246500' => 'mdo', 'MD12G1246700' => 'mdo', 'Medtr1g080250' => 'mtr', 'Medtr5g010470' => 'mtr', 'Medtr7g115550' => 'mtr', 'Medtr7g115690' => 'mtr', 'MELO3C004421.2' => 'cme', 'MELO3C010162.2' => 'cme', 'MELO3C017520.2' => 'cme', 'MELO3C017522.2' => 'cme', 'Migut.B01119' => 'egut', 'Migut.F00802' => 'egut', 'Migut.F01544' => 'egut', 'Migut.F01545' => 'egut', 'MSTRG.27376' => 'ama', 'Nitab4.5_0000380g0020' => 'nta', 'Nitab4.5_0000409g0100' => 'nta', 'Nitab4.5_0003768g0030' => 'nta', 'Nitab4.5_0003780g0010' => 'nta', 'Nitab4.5_0009204g0020' => 'nta', 'Nitab4.5_0012737g0010' => 'nta', 'Nitab4.5_0018899g0010' => 'nta', 'Nn1g02790' => 'nnu', 'Nn3g19672' => 'nnu', 'Nn3g19673' => 'nnu', 'Nn5g29018' => 'nnu', 'Oeu012234.1' => 'oeu', 'Oeu012236.3' => 'oeu', 'Oeu016025.3' => 'oeu', 'Oeu025620.1' => 'oeu', 'Os04g0348300' => 'osa', 'Os04g0516600' => 'osa', 'Peaxi162Scf00135g00038' => 'pax', 'Peaxi162Scf00135g00312' => 'pax', 'Peaxi162Scf00135g00313' => 'pax', 'Peaxi162Scf00304g00074' => 'pax', 'Peaxi162Scf00304g00075' => 'pax', 'PGR004G0855' => 'pgr', 'PGR031G3359' => 'pgr', 'PGSC0003DMG400011499' => 'stu', 'PGSC0003DMG400011500' => 'stu', 'Phvul.004G090900' => 'pvu', 'Phvul.006G105400' => 'pvu', 'Phvul.L001860' => 'pvu', 'Phvul.L002060' => 'pvu', 'Potri.013G046300' => 'ptr', 'Potri.013G046400' => 'ptr', 'Potri.019G018400' => 'ptr', 'Potri.019G018500' => 'ptr', 'Pp3c3_17580' => 'ppa', 'Pp3c4_31180' => 'ppa', 'PRCOL_00004307' => 'pco', 'Prupe.6G349400' => 'ppe', 'Prupe.6G349500' => 'ppe', 'Psat3g006560' => 'psa', 'Psat3g006920' => 'psa', 'Psat6g142560' => 'psa', 'PSO017G2945' => 'pso', 'PSO063G2917' => 'pso', 'PSO210G0556' => 'pso', 'PSO210G1138' => 'pso', 'PSO832G2234' => 'pso', 'PSO832G3554' => 'pso', 'QL03p030803' => 'qlo', 'QL03p030821' => 'qlo', 'QL10p043041' => 'qlo', 'QL10p043044' => 'qlo', 'RcHm_v2.0_Chr3g0449781' => 'rch', 'RcHm_v2.0_Chr3g0449801' => 'rch', 'RcHm_v2.0_Chr5g0032281' => 'rch', 'RcHm_v2.0_Chr6g0265461' => 'rch', 'Rhsim05G0174800' => 'rsi', 'Rhsim05G0174900' => 'rsi', 'Rhsim05G0175000' => 'rsi', 'Rhsim05G0215100' => 'rsi', 'Rhsim09G0137500' => 'rsi', 'Sabra13G0042500' => 'sbr', 'Sabra13G0117500' => 'sbr', 'Sabra19G0028000' => 'sbr', 'Sabra19G0028300' => 'sbr', 'Sabra19G0030400' => 'sbr', 'Sabra19G0030500' => 'sbr', 'Sabra19G0030600' => 'sbr', 'Sabra19G0030700' => 'sbr', 'Sabra19G0030800' => 'sbr', 'Sabra19G0030900' => 'sbr', 'Sabra19G0031000' => 'sbr', 'Sabra19G0031500' => 'sbr', 'SalBow1G0011' => 'sbo', 'SalBow3G0432' => 'sbo', 'Sc03g0006090' => 'sci', 'Sc03g0006100' => 'sci', 'Sc03g0006690' => 'sci', 'Sc03g0006700' => 'sci', 'Sc08g0009190' => 'sci', 'Sc20g0000600' => 'sci', 'Sed0000116' => 'sed', 'Sed0003092' => 'sed', 'Sed0024923' => 'sed', 'Sed0025121' => 'sed', 'SEGI_17278' => 'sgi', 'SEGI_17303' => 'sgi', 'SEGI_20641' => 'sgi', 'SEGI_32323' => 'sgi', 'SEGI_38835' => 'sgi', 'SGA_v2.0_scaffold10G05255' => 'sas', 'SGA_v2.0_scaffold1G00525' => 'sas', 'SGA_v2.0_scaffold4559G54503' => 'sas', 'SHI00615' => 'shi', 'SMO145G0281' => 'smo', 'SMO196G0113' => 'smo', 'SMO196G0150' => 'smo', 'SMO196G0202' => 'smo', 'SMO196G0272' => 'smo', 'SMO234G0003' => 'smo', 'SMO234G0053' => 'smo', 'Solyc04g009950.3' => 'sly', 'Solyc04g009960.3' => 'sly', 'Sopen04g005080' => 'spe', 'Sopen04g005090' => 'spe', 'Sp1g07290' => 'spa', 'Sp1g08360' => 'spa', 'Sp3g03370' => 'spa', 'TAR362G0490' => 'tar', 'TAR362G0879' => 'tar', 'TAR633G2333' => 'tar', 'THA.LOC104799712' => 'tha', 'THA.LOC104805779' => 'tha', 'THA.LOC104823762' => 'tha', 'THA.LOC104823763' => 'tha', 'Thecc.05G271400' => 'tca', 'Thecc.05G271600' => 'tca', 'Thhalv10001097m.g' => 'esa', 'Thhalv10006800m.g' => 'esa', 'Thhalv10008026m.g' => 'esa', 'Thhalv10021036m.g' => 'esa', 'TPR.G22328' => 'tpr', 'TPR.G40365' => 'tpr', 'TPR.G6921' => 'tpr', 'TPR.G6939' => 'tpr', 'TWI31G0266' => 'twi', 'TWI56G1236' => 'twi', 'TWI79G0745' => 'twi', 'unitig_0.g2788' => 'ugi', 'unitig_37.g12443' => 'ugi', 'unitig_46.g18728' => 'ugi', 'unitig_747.g21794' => 'ugi', 'unitig_899.g14634' => 'ugi', 'vmacro10359' => 'vma', 'vmacro19997' => 'vma', 'vmacro19998' => 'vma', 'vmacro19999' => 'vma', 'VMungo0464G0145' => 'vmu', 'VMungo0540G2096' => 'vmu', 'VMungo0720G0124' => 'vmu', 'VMungo1309G2705' => 'vmu', 'Zm00001eb017590' => 'zma', 'Zm00001eb077630' => 'zma', 'Zm00001eb077640' => 'zma', 'Zm00001eb142770' => 'zma', 'Zm00001eb212490' => 'zma', 'Zm00001eb426650' => 'zma' ) $gf_id = 'HOM05D001473' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001473' ) $data_identifier = 'HOM05D001473' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 6, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 16, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 2, 'cil' => (int) 2, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 2, 'csa' => (int) 9, 'camsi' => (int) 13, 'dca' => (int) 3, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 5, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 8, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 3, 'lsa' => (int) 8, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 1, 'mco' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 12, 'sbo' => (int) 2, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 7, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426650' $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